Abstract

Our genes are made up of hundreds to millions of building blocks, called DNA nucleotides, and if
just a single nucleotide of DNA becomes mutated it might cause a devastating genetic disease. But
sometimes a mutation actually does no damage. What kinds of mutations have to occur to cause a genetic disease?
In this science project, you will explore online genetic databases to identify how a mutation in a gene
can result in a dysfunctional protein, and how other mutations may have no effect at all.

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Introduction

The Human Genome Project has estimated that the human genome contains around 20,000 to 25,000 genes. Each of these genes is made up of hundreds to millions of DNA nucleotides. Sometimes only a single DNA mutation (change in the DNA sequence) can cause a person to have a devastating genetic disease, and researchers have been able to identify mutations responsible for causing thousands of different genetic diseases and conditions. But sometimes a DNA mutation may do no harm at all. It all has to do with what the DNA mutation is and where it is located.

Every gene in the human body consists of DNA (deoxyribonucleic acid). DNA is a genetic code that is made up of four different types of nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C). This DNA code is turned into RNA (ribonucleic acid) in our bodies in a process called transcription. In RNA, a nucleotide called uracil substitutes for every thymine. The RNA then goes through a process called translation to turn into amino acids. During translation, every three RNA nucleotides code for a single amino acid. This set of three nucleotides is called a "codon," and different codons may code for the same amino acid. In the end, a sequence of DNA has been turned into a sequence of amino acids joined together in a long chain, which is called a protein. Proteins are responsible for most of the functions of our cells.

Many things can happen during this process to prevent a gene from turning into protein or to have a non-functional protein created. In a gene, if a single DNA nucleotide is mutated, for example from an adenine (A) to a guanine (G), this may cause the wrong amino acid to be made. If the wrong amino acid is made and assembled into a long chain of amino acids, the resulting protein may not work. This is because different amino acids are different in many ways, such as size and in the electric charges they have. These different characteristics affect how they interact with each other as well as the other molecules that surround them (such as other amino acids and water). For example, positively and negatively charged molecules prefer to interact with each other and with water, which is called being hydrophilic, whereas nonpolar molecules do not like to interact with charged molecules or with water, which is called being hydrophobic. These seemingly small differences can have very large consequences.

For example, in cystic fibrosis there is a mutation in a gene, called the CFTR gene, that encodes for a channel that controls the flow of particles in cells. Specifically, this channel normally regulates whether small negatively charged particles, called chloride ions, can flow into, or flow out of, the cells. The movement of charged particles acts to balance the flow of water into, and out of, the cells. In people with cystic fibrosis, the mutated CFTR gene creates a channel that does not function, and consequently the flow of water in tissues is abnormal. In turn, the abnormal flow of water causes a build up of thick mucus on the lining of many internal organs and can have many other devastating effects on different parts of the body (see Figure 1).

Figure 1.
Cystic fibrosis is caused by a mutation in the CFTR gene, which encodes for a chloride channel that is important for regulating water flow into, and out of, the cells. Because so many bodily functions rely on normal water flow, a disruption in water flow can cause a number of devastating effects, as shown in the "Manifestations of Cystic Fibrosis" image (Wikimedia Commons, 2011)

While DNA mutations clearly cause a number of genetic diseases, some DNA mutations may not be problematic. In this science project, you will investigate cystic fibrosis and the genetic mutations that cause it, using online genetic databases. This investigation will allow you to determine what type of mutations may alter the function of a protein and which ones may have little or no effect.

Terms and Concepts

Genes

DNA

Mutation

Genetic disease

Nucleotides

RNA

Transcription

Translation

Amino acids

Codon

Hydrophilic

Hydrophobic

Allele

Questions

How does a gene become a protein?

In a given gene, what kind of DNA mutation would not change the protein that is made?

What makes some amino acids hydrophobic and others hydrophilic?

How common are mutations in the human genome? Is it very likely or very unlikely that your DNA carries any mutations?

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Materials and Equipment

Computer with an Internet connection

Lab notebook

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Experimental Procedure

Determining How a Disease Gene Is Mutated

This science project focuses on the genetic disease cystic fibrosis, but you can do it with any genetic
disease you would like to choose. See the Variations section and Table 2 for information on doing this
science project with genetic diseases other than cystic fibrosis.

First, go to the
Genetics Home Reference Tutorial
and follow the steps through the section titled "How can I find more information about a specific genetic condition?"

On step 4 of the tutorial section, read through the entry on the genetic disease, paying special attention to the genetic changes that cause the disease.

What does the entry on cystic fibrosis tell you about its genetic causes? How are the chloride channels different in cystic fibrosis, and how does this affect the body as a whole?

On step 4 of the tutorial section, read about the CFTR gene and how it is involved in cystic fibrosis.

What family of genes does the CFTR gene belong to?

What chromosome is the CFTR gene located on?

What amino acids in the CFTR gene are commonly mutated to cause cystic fibrosis?

Continue through steps 5 and 6 of the tutorial section, and read about the gene families related to cystic fibrosis.

What roles do the genes belonging to this family usually carry out in the cell?

What do all of the genes in the same family have in common?

From DNA to Amino Acids

Once you have the tutorial information on cystic fibrosis, you can figure out if and how a simple mutation in
the DNA ended up changing the amino acids that are made, as well as the function of the entire protein.
Table 1 has been partly filled in with information on non-pathogenic alleles of the CFTR gene.
Alleles are alternative forms of a gene that occur through mutation of the DNA. Non-pathogenic
alleles are alleles that have been shown to not cause cystic fibrosis. They are mutations that do not
affect if a person gets the disease or not. This is the opposite of pathogenic alleles, which are alleles
that are known to be harmful and actually cause the disease. In this part of the science project, you will
be filling in the rest of Table 1 with additional information on these non-pathogenic alleles. You will also
select ten pathogenic alleles and fill in their information in the remaining empty rows in Table 1.

Go through the tutorial until you reach the section titled "I want to look up a gene involved in a genetic disease and find out how it is mutated in that disease. How can I do this?," and are on step 2a.

After sorting by "Clinical interpretation" in step 2a, click forward through the pages until you see "pathogenic" (not just "probable-pathogenic") listed as the "Clinical interpretation." You may need to skip through several pages.

Pick ten alleles that have both "SNC" listed as their "Var Class" (on the far left) and "pathogenic" as their "Clinical interpretation." ("SNC" means the allele has a single nucleotide change.)

In your notebook, fill out Table 1 with the following information on the 10 pathogenic alleles:

The "Transcript," which lists what the DNA mutation is. Put this information in the "Transcript Mutation" column in Table 1.

The "rs id." This is an identifier for this allele.

Continue with step 3 of the tutorial section by clicking on the "rs id" link for each of the ten alleles you picked.

First check to make sure that there is a "Residue change" listed here that matches the "Protein" information listed on the previous page for the allele.

Record the corresponding "Allele change" for each of the ten alleles in your notebook. Put this in the "Codon Sequence Change (DNA)" column of Table 1. This is the DNA nucleotide that has changed.

Transcript Mutation

rsID

Codon Sequence Change (DNA)

Codon Sequence Change (mRNA)

Amino Acid Sequence Change

Effect

Pathogenic or Non-Pathogenic

1408G>A

rs213950

GTG → ATG

GUG → AUG

V [Val] → M [Met]

Changes from a neutral, nonpolar amino acid to another neutral, nonpolar amino acid.

Non-Pathogenic

1516A>G

rs1800091

ATC → GTC

Non-Pathogenic

4002A>G

N/A

CCA → CCG

Non-Pathogenic

2694T>G

N/A

ACT → ACG

Non-Pathogenic

4521G>A

N/A

CAG → CAA

Non-Pathogenic

Pathogenic

Pathogenic

Pathogenic

Pathogenic

Pathogenic

Pathogenic

Pathogenic

Pathogenic

Pathogenic

Pathogenic

Table 1. This table contains information on five CFTR alleles that are known to not be pathogenic. Some of these alleles were taken from published scientific studies (see the Bibliography for the citations) and do not have assigned rsIDs (these are labeled "N/A").
For the first allele, all of the relevant information has been entered as an example. For the next four non-pathogenic alleles, fill in the information in the empty cells. Pick ten pathogenic alleles, and enter their information into the table as well.

Convert the DNA sequence to mRNA, by changing every T to a U, and record this in your notebook in Table 1, under the "Codon Sequence Change (mRNA)" column.

For example, GAG would still be GAG, and GTG would convert to GUG.

Be sure to do this for the non-pathogenic alleles as well.

To determine if and how the DNA change caused a change in the amino acid the gene makes, look at Figure 2.

Record the amino acid sequence change in Table 1 under the "Amino Acid Sequence Change" column.

Be sure to do this for the non-pathogenic alleles as well.

This entry should match the "Residue change" that you observed in step 2f.

What DNA mutations would not have caused a change in the amino acid that is made?

Do any of the non-pathogenic alleles have such a DNA mutation?

On the gene SNP page, scroll down to "Fasta sequence."

The Fasta sequence is the complete DNA sequence of the gene. You should be able to pick out where the mutated nucleotide is because the sequence will be interrupted by a letter all on its own line (the letter will not be a DNA nucleotide letter, but will be some other letter, such as an "N" or an "R"). This letter shows the location of the mutated nucleotide.

What would have happened if the mutated nucleotide had instead been one of the nucleotides immediately adjacent to the actual mutated nucleotide?

Figure 2.
A DNA sequence is converted into mRNA, and every three mRNA nucleotides (called "codons") code for a certain amino acid. This figure shows what mRNA codons code for what amino acids. A protein is made up of a sequence of several specific amino acids. Consequently, a gene's mutated DNA can ultimately change the function of the protein that results (image courtesy of Schering-Plough).

Testing How the Mutation Matters

You now know which amino acids are mutated in the genetic disease you're interested in, and how they became that way, but why is this mutation so damaging to the normal structure of the protein?

For each allele, look at the "Amino Acid Sequence Change" you entered in Table 1.

Look at Table 2 to determine how the normal amino acid and the mutant amino acid are different from each other.

Record in your notebook in Table 1, under the column labeled "Effect," what the differences are between the normal and mutant amino acids.

Be sure to do this for the non-pathogenic alleles as well.

How do you think these differences affect how the protein as a whole functions?

Why do you think the non-pathogenic alleles do not disrupt the protein's function?

Electric Charge

Full Amino Acid Name

3-Letter Name

1-Letter Name

Nonpolar Amino Acids

Alanine

Ala

A

Glycine

Gly

G

Isoleucine

Ile

I

Leucine

Leu

L

Methionine

Met

M

Valine

Val

V

Nonpolar Uncharged Amino Acids

Asparagine

Asn

N

Cysteine

Cys

C

Glutamine

Gln

Q

Proline

Pro

P

Serine

Ser

S

Threonine

Thr

T

Aromatic Amino Acids

Phenylalanine

Phe

F

Tryptophan

Trp

W

Tyrosine

Tyr

Y

Positively Charged Amino Acids

Arginine

Arg

R

Histidine

His

H

Lysine

Lys

K

Negatively Charged Amino Acids

Aspartic Acid

Asp

D

Glutamic Acid

Glu

E

Table 2. Amino acids vary in whether they have an electric charge or have no charge. If they do have a charge, it can be positive or negative. They also vary in size. All of these factors affect how the amino acids interact with other amino acids in the same protein, and with other molecules, such as water, that are surrounding them. For more information,
see this website: http://www.russelllab.org/aas/

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Variations

Now that you know how to find how a gene mutation can cause a specific genetic disease, repeat the
Experimental Procedure for other genetic diseases, such as sickle cell disease, hemochromatosis, or
others listed in Table 3. Different amounts of information may be available for different diseases,
and you may need to adjust the Experimental Procedure for some of these diseases. When investigating genetic
diseases other than cystic fibrosis, you do not need to include non-pathogenic alleles.

Genetic Diseases

Cystic fibrosis

Sickle cell disease

Hemochromatosis

Hemophilia

Factor V Leiden thrombophilia

Pompe disease

Neurofibromatosis type 1

Lynch syndrome

Parkinson's disease

Crohn disease

Amyotrophic lateral sclerosis (Lou Gehrig's Disease)

Tourette syndrome

Bloom syndrome

Canavan disease

Gaucher disease

Niemann-Pick disease

Tay-Sachs disease

X-linked dystonia-parkinsonism

Table 3. These well-studied genetic diseases and conditions have large amounts of data available on their genetic causes.

If you repeat this project with a genetic disease other than cystic fibrosis, try doing a literature search for non-pathogenic alleles of the gene responsible for the disease. Incorporate the non-pathogenic alleles in to your project, and explain why they do not appear to be pathogenic while other mutations are. For help searching the literature read the guide to
Resources for Finding and Accessing Scientific Literature.
You may also find you need some help from someone experienced with genetics or bioinformatics to understand
How to Read a Scientific Paper.

While some gene mutations cause visible genetic diseases, other gene mutations do not significantly change the function of the protein.

Looking at Figure 2 showing the amino acids that the different mRNA codons code for, what would be a less damaging DNA mutation?

Looking at Table 2 and the link in its caption, what kind of amino acid mutations would be less likely to change a protein's normal function?

Ask an Expert

The Ask an Expert Forum is intended to be a place where students can go to find answers to science questions that they have been unable to find using other resources. If you have specific questions about your science fair project or science fair, our team of volunteer scientists can help. Our Experts won't do the work for you, but they will make suggestions, offer guidance, and help you troubleshoot.

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